There is an increasing amount of research into the impact of family breakdown on children. The Australian Institute of Family Studies has collated a number of the most recent studies here.
Though the conclusions of individual studies vary considerably, children exposed to a family breakdown generally do significantly worse than children in intact families on a majority of factors tested. The sample sizes of some studies are large enough to exclude the effect (or control for) different family types or socio-economic status. If successful co-parenting is achieved after a family separation, this may largely mitigate otherwise likely adverse outcomes for children.